src/jalview/jbgui/GAlignFrame.java

   1 /********************
   2  * 2004 Jalview Reengineered
   3  * Barton Group
   4  * Dundee University
   5  *
   6  * AM Waterhouse
   7  *******************/
   8
   9 package jalview.jbgui;
  10
  11 import javax.swing.*;
  12 import java.awt.event.*;
  13 import java.awt.*;
  14
  15 public class GAlignFrame extends JInternalFrame
  16 {
  17   protected JMenuBar alignFrameMenuBar = new JMenuBar();
  18   protected JMenu fileMenu = new JMenu();
  19   protected JMenuItem closeMenuItem = new JMenuItem();
  20   protected JMenu editMenu = new JMenu();
  21   protected JMenu viewMenu = new JMenu();
  22   protected JMenu colourMenu = new JMenu();
  23   protected JMenu calculateMenu = new JMenu();
  24   protected JMenu alignMenu = new JMenu();
  25   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
  26   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
  27   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
  28   protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();
  29   protected JMenuItem remove2LeftMenuItem = new JMenuItem();
  30   protected JMenuItem remove2RightMenuItem = new JMenuItem();
  31   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
  32   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
  33   protected JMenuItem setGapCharMenuItem = new JMenuItem();
  34   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
  35   protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
  36   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
  37   protected JMenuItem sortIDMenuItem = new JMenuItem();
  38   protected JMenuItem sortGroupMenuItem = new JMenuItem();
  39   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
  40   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
  41   protected JMenuItem PCAMenuItem = new JMenuItem();
  42   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
  43   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
  44   protected JMenuItem clustalAlignMenuItem = new JMenuItem();
  45   protected JMenuItem msaAlignMenuItem = new JMenuItem();
  46   BorderLayout borderLayout1 = new BorderLayout();
  47   public JLabel statusBar = new JLabel();
  48   protected JMenu saveAlignmentMenu = new JMenu();
  49   protected JMenu outputTextboxMenu = new JMenu();
  50   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
  51   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
  52   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
  53   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
  54   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
  55   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
  56   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
  57   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
  58   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
  59   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
  60   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
  61   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
  62   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
  63   protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
  64   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
  65   JMenuItem htmlMenuItem = new JMenuItem();
  66   JMenuItem overviewMenuItem = new JMenuItem();
  67   protected JMenuItem undoMenuItem = new JMenuItem();
  68   protected JMenuItem redoMenuItem = new JMenuItem();
  69   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
  70   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
  71   protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
  72   JMenuItem printMenuItem = new JMenuItem();
  73   protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
  74   JMenuItem findMenuItem = new JMenuItem();
  75   JMenu searchMenu = new JMenu();
  76   protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
  77   protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
  78   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
  79   JMenuItem deleteGroups = new JMenuItem();
  80   JMenuItem delete = new JMenuItem();
  81   JMenuItem copy = new JMenuItem();
  82   JMenuItem cut = new JMenuItem();
  83   JMenu jMenu1 = new JMenu();
  84   JMenuItem pasteNew = new JMenuItem();
  85   JMenuItem pasteThis = new JMenuItem();
  86   protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
  87   JMenuItem createPNG = new JMenuItem();
  88   protected JMenuItem font = new JMenuItem();
  89   protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
  90   JMenuItem epsFile = new JMenuItem();
  91   JMenuItem LoadtreeMenuItem = new JMenuItem();
  92   JMenuItem jpred = new JMenuItem();
  93   protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
  94   protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
  95   protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
  96   JMenuItem modifyPID = new JMenuItem();
  97   JMenuItem modifyConservation = new JMenuItem();
  98   protected JMenu sortByTreeMenu = new JMenu();
  99   public GAlignFrame()
 100   {
 101
 102
 103     try
 104     {
 105       jbInit();
 106       setJMenuBar(alignFrameMenuBar);
 107
 108       JMenuItem item;
 109       // dynamically fill save as menu with available formats
 110       for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
 111         item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
 112         saveAlignmentMenu.add( item );
 113         item.addActionListener(new java.awt.event.ActionListener()
 114         {
 115           public void actionPerformed(ActionEvent e)
 116           {
 117             saveAs_actionPerformed(e);
 118           }
 119         });
 120
 121         item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
 122         item.addActionListener(new java.awt.event.ActionListener()
 123         {
 124           public void actionPerformed(ActionEvent e)
 125           {
 126             outputText_actionPerformed(e);
 127           }
 128         });
 129
 130         outputTextboxMenu.add( item );
 131       }
 132
 133     }
 134     catch(Exception e)
 135     {
 136       e.printStackTrace();
 137     }
 138
 139     ButtonGroup colours = new ButtonGroup();
 140     colours.add(noColourmenuItem);
 141     colours.add(clustalColour);
 142     colours.add(zappoColour);
 143     colours.add(taylorColour);
 144     colours.add(hydrophobicityColour);
 145     colours.add(helixColour);
 146     colours.add(strandColour);
 147     colours.add(turnColour);
 148     colours.add(buriedColour);
 149     colours.add(userDefinedColour);
 150     colours.add(PIDColour);
 151     colours.add(BLOSUM62Colour);
 152     colours.add(nucleotideColour);
 153   }
 154   private void jbInit() throws Exception
 155   {
 156     fileMenu.setMnemonic('F');
 157     fileMenu.setText("File");
 158     saveAlignmentMenu.setMnemonic('L');
 159     saveAlignmentMenu.setText("Save alignment to local file");
 160     closeMenuItem.setMnemonic('C');
 161     closeMenuItem.setText("Close");
 162     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
 163     {
 164       public void actionPerformed(ActionEvent e)
 165       {
 166         closeMenuItem_actionPerformed(e);
 167       }
 168     });
 169     editMenu.setText("Edit");
 170     viewMenu.setText("View");
 171     colourMenu.setText("Colour");
 172     calculateMenu.setText("Calculate");
 173     alignMenu.setText("Web Service");
 174     selectAllSequenceMenuItem.setText("Select all");
 175     selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
 176     {
 177       public void actionPerformed(ActionEvent e)
 178       {
 179         selectAllSequenceMenuItem_actionPerformed(e);
 180       }
 181     });
 182     deselectAllSequenceMenuItem.setText("Clear selection");
 183     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
 184     {
 185       public void actionPerformed(ActionEvent e)
 186       {
 187         deselectAllSequenceMenuItem_actionPerformed(e);
 188       }
 189     });
 190     invertSequenceMenuItem.setText("Invert sequence selection");
 191     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
 192     {
 193       public void actionPerformed(ActionEvent e)
 194       {
 195         invertSequenceMenuItem_actionPerformed(e);
 196       }
 197     });
 198     deselectAllColumnsMenuItem.setText("Deselect all columns");
 199     deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
 200     {
 201       public void actionPerformed(ActionEvent e)
 202       {
 203         deselectAllColumnsMenuItem_actionPerformed(e);
 204       }
 205     });
 206     remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
 207     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
 208     {
 209       public void actionPerformed(ActionEvent e)
 210       {
 211         remove2LeftMenuItem_actionPerformed(e);
 212       }
 213     });
 214     remove2RightMenuItem.setText("Remove sequence -> right of selected column");
 215     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
 216     {
 217       public void actionPerformed(ActionEvent e)
 218       {
 219         remove2RightMenuItem_actionPerformed(e);
 220       }
 221     });
 222     removeGappedColumnMenuItem.setText("Remove gapped columns");
 223     removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
 224     {
 225       public void actionPerformed(ActionEvent e)
 226       {
 227         removeGappedColumnMenuItem_actionPerformed(e);
 228       }
 229     });
 230     removeAllGapsMenuItem.setText("Remove all gaps");
 231     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
 232     {
 233       public void actionPerformed(ActionEvent e)
 234       {
 235         removeAllGapsMenuItem_actionPerformed(e);
 236       }
 237     });
 238     setGapCharMenuItem.setText("Set gap character to \".\"");
 239     setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()
 240     {
 241       public void actionPerformed(ActionEvent e)
 242       {
 243         setGapCharMenuItem_actionPerformed(e);
 244       }
 245     });
 246     viewBoxesMenuItem.setText("Boxes");
 247     viewBoxesMenuItem.setState(true);
 248     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
 249     {
 250       public void actionPerformed(ActionEvent e)
 251       {
 252         viewBoxesMenuItem_actionPerformed(e);
 253       }
 254     });
 255     viewTextMenuItem.setText("Text");
 256     viewTextMenuItem.setState(true);
 257     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 258     {
 259       public void actionPerformed(ActionEvent e)
 260       {
 261         viewTextMenuItem_actionPerformed(e);
 262       }
 263     });
 264     sortPairwiseMenuItem.setText("Sort by pairwise identity");
 265     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
 266     {
 267       public void actionPerformed(ActionEvent e)
 268       {
 269         sortPairwiseMenuItem_actionPerformed(e);
 270       }
 271     });
 272     sortIDMenuItem.setText("Sort by ID");
 273     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
 274     {
 275       public void actionPerformed(ActionEvent e)
 276       {
 277         sortIDMenuItem_actionPerformed(e);
 278       }
 279     });
 280     sortGroupMenuItem.setText("Sort by group");
 281     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
 282     {
 283       public void actionPerformed(ActionEvent e)
 284       {
 285         sortGroupMenuItem_actionPerformed(e);
 286       }
 287     });
 288     removeRedundancyMenuItem.setText("Remove redundancy");
 289     removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
 290     {
 291       public void actionPerformed(ActionEvent e)
 292       {
 293         removeRedundancyMenuItem_actionPerformed(e);
 294       }
 295     });
 296     pairwiseAlignmentMenuItem.setText("Pairwise alignments");
 297     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
 298     {
 299       public void actionPerformed(ActionEvent e)
 300       {
 301         pairwiseAlignmentMenuItem_actionPerformed(e);
 302       }
 303     });
 304     PCAMenuItem.setText("Principal component analysis");
 305     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
 306     {
 307       public void actionPerformed(ActionEvent e)
 308       {
 309         PCAMenuItem_actionPerformed(e);
 310       }
 311     });
 312     averageDistanceTreeMenuItem.setText("Average distance tree using PID");
 313     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
 314     {
 315       public void actionPerformed(ActionEvent e)
 316       {
 317         averageDistanceTreeMenuItem_actionPerformed(e);
 318       }
 319     });
 320     neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
 321     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
 322     {
 323       public void actionPerformed(ActionEvent e)
 324       {
 325         neighbourTreeMenuItem_actionPerformed(e);
 326       }
 327     });
 328     clustalAlignMenuItem.setText("Clustal alignment");
 329     clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
 330     {
 331       public void actionPerformed(ActionEvent e)
 332       {
 333         clustalAlignMenuItem_actionPerformed(e);
 334       }
 335     });
 336     msaAlignMenuItem.setText("Muscle alignment");
 337     msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
 338     {
 339       public void actionPerformed(ActionEvent e)
 340       {
 341         msaAlignMenuItem_actionPerformed(e);
 342       }
 343     });
 344     this.getContentPane().setLayout(borderLayout1);
 345     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
 346     statusBar.setBackground(Color.white);
 347     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
 348     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
 349     statusBar.setText("Status bar");
 350     outputTextboxMenu.setMnemonic('T');
 351     outputTextboxMenu.setText("Output alignment via textbox");
 352     clustalColour.setSelected(false);
 353     clustalColour.setText("Clustalx colours");
 354     clustalColour.addActionListener(new java.awt.event.ActionListener()
 355     {
 356       public void actionPerformed(ActionEvent e)
 357       {
 358         clustalColour_actionPerformed(e);
 359       }
 360     });
 361     zappoColour.setText("Zappo colour scheme");
 362     zappoColour.addActionListener(new java.awt.event.ActionListener()
 363     {
 364       public void actionPerformed(ActionEvent e)
 365       {
 366         zappoColour_actionPerformed(e);
 367       }
 368     });
 369     taylorColour.setText("Taylor colour scheme");
 370     taylorColour.addActionListener(new java.awt.event.ActionListener()
 371     {
 372       public void actionPerformed(ActionEvent e)
 373       {
 374         taylorColour_actionPerformed(e);
 375       }
 376     });
 377     hydrophobicityColour.setText("By hydrophobicity");
 378     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
 379     {
 380       public void actionPerformed(ActionEvent e)
 381       {
 382         hydrophobicityColour_actionPerformed(e);
 383       }
 384     });
 385     helixColour.setText("Helix propensity");
 386     helixColour.addActionListener(new java.awt.event.ActionListener()
 387     {
 388       public void actionPerformed(ActionEvent e)
 389       {
 390         helixColour_actionPerformed(e);
 391       }
 392     });
 393     strandColour.setText("Strand propensity");
 394     strandColour.addActionListener(new java.awt.event.ActionListener()
 395     {
 396       public void actionPerformed(ActionEvent e)
 397       {
 398         strandColour_actionPerformed(e);
 399       }
 400     });
 401     turnColour.setText("Turn propensity");
 402     turnColour.addActionListener(new java.awt.event.ActionListener()
 403     {
 404       public void actionPerformed(ActionEvent e)
 405       {
 406         turnColour_actionPerformed(e);
 407       }
 408     });
 409     buriedColour.setText("Buried index");
 410     buriedColour.addActionListener(new java.awt.event.ActionListener()
 411     {
 412       public void actionPerformed(ActionEvent e)
 413       {
 414         buriedColour_actionPerformed(e);
 415       }
 416     });
 417     userDefinedColour.setText("User defined colours");
 418     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
 419     {
 420       public void actionPerformed(ActionEvent e)
 421       {
 422         userDefinedColour_actionPerformed(e);
 423       }
 424     });
 425     PIDColour.setText("Percentage Identity");
 426     PIDColour.addActionListener(new java.awt.event.ActionListener()
 427     {
 428       public void actionPerformed(ActionEvent e)
 429       {
 430         PIDColour_actionPerformed(e);
 431       }
 432     });
 433     BLOSUM62Colour.setText("BLOSUM62 score");
 434     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
 435     {
 436       public void actionPerformed(ActionEvent e)
 437       {
 438         BLOSUM62Colour_actionPerformed(e);
 439       }
 440     });
 441     avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
 442     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
 443     {
 444       public void actionPerformed(ActionEvent e)
 445       {
 446         avTreeBlosumMenuItem_actionPerformed(e);
 447       }
 448     });
 449     njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
 450     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
 451     {
 452       public void actionPerformed(ActionEvent e)
 453       {
 454         njTreeBlosumMenuItem_actionPerformed(e);
 455       }
 456     });
 457     annotationPanelMenuItem.setActionCommand("");
 458     annotationPanelMenuItem.setText("Annotation Panel");
 459     annotationPanelMenuItem.setState(true);
 460     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
 461     {
 462       public void actionPerformed(ActionEvent e)
 463       {
 464         annotationPanelMenuItem_actionPerformed(e);
 465       }
 466     });
 467     colourTextMenuItem.setText("Colour text");
 468     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
 469     {
 470       public void actionPerformed(ActionEvent e)
 471       {
 472         colourTextMenuItem_actionPerformed(e);
 473       }
 474     });
 475     htmlMenuItem.setText("Output as HTML");
 476     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
 477     {
 478       public void actionPerformed(ActionEvent e)
 479       {
 480         htmlMenuItem_actionPerformed(e);
 481       }
 482     });
 483     overviewMenuItem.setText("Overview window");
 484     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
 485     {
 486       public void actionPerformed(ActionEvent e)
 487       {
 488         overviewMenuItem_actionPerformed(e);
 489       }
 490     });
 491     undoMenuItem.setEnabled(false);
 492     undoMenuItem.setMnemonic('Z');
 493     undoMenuItem.setText("Undo");
 494     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
 495     {
 496       public void actionPerformed(ActionEvent e)
 497       {
 498         undoMenuItem_actionPerformed(e);
 499       }
 500     });
 501     redoMenuItem.setEnabled(false);
 502     redoMenuItem.setMnemonic('0');
 503     redoMenuItem.setText("Redo");
 504     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
 505     {
 506       public void actionPerformed(ActionEvent e)
 507       {
 508         redoMenuItem_actionPerformed(e);
 509       }
 510     });
 511     conservationMenuItem.setText("By conservation");
 512     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
 513     {
 514       public void actionPerformed(ActionEvent e)
 515       {
 516         conservationMenuItem_actionPerformed(e);
 517       }
 518     });
 519     noColourmenuItem.setText("None");
 520     noColourmenuItem.setSelected(true);
 521     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
 522     {
 523       public void actionPerformed(ActionEvent e)
 524       {
 525         noColourmenuItem_actionPerformed(e);
 526       }
 527     });
 528     wrapMenuItem.setText("Wrap alignment");
 529     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
 530     {
 531       public void actionPerformed(ActionEvent e)
 532       {
 533         wrapMenuItem_actionPerformed(e);
 534       }
 535     });
 536     printMenuItem.setText("Print");
 537     printMenuItem.addActionListener(new java.awt.event.ActionListener()
 538     {
 539       public void actionPerformed(ActionEvent e)
 540       {
 541         printMenuItem_actionPerformed(e);
 542       }
 543     });
 544     renderGapsMenuItem.setText("Render gaps");
 545     renderGapsMenuItem.setState(true);
 546     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
 547     {
 548       public void actionPerformed(ActionEvent e)
 549       {
 550         renderGapsMenuItem_actionPerformed(e);
 551       }
 552     });
 553     findMenuItem.setText("Find");
 554     findMenuItem.addActionListener(new java.awt.event.ActionListener()
 555     {
 556       public void actionPerformed(ActionEvent e)
 557       {
 558         findMenuItem_actionPerformed(e);
 559       }
 560     });
 561     searchMenu.setText("Search");
 562
 563     abovePIDThreshold.setText("Above PID threshold");
 564     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
 565       public void actionPerformed(ActionEvent e) {
 566         abovePIDThreshold_actionPerformed(e);
 567       }
 568     });
 569     sequenceFeatures.setText("Sequence Features");
 570     sequenceFeatures.addActionListener(new ActionListener()
 571     {
 572       public void actionPerformed(ActionEvent actionEvent)
 573       {
 574         sequenceFeatures_actionPerformed(actionEvent);
 575       }
 576     });
 577     nucleotideColour.setText("Nucleotide colours");
 578     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
 579     {
 580       public void actionPerformed(ActionEvent e)
 581       {
 582         nucleotideColour_actionPerformed(e);
 583       }
 584     });
 585     deleteGroups.setSelected(false);
 586     deleteGroups.setText("Delete all groups");
 587     deleteGroups.addActionListener(new java.awt.event.ActionListener()
 588     {
 589       public void actionPerformed(ActionEvent e)
 590       {
 591         deleteGroups_actionPerformed(e);
 592       }
 593     });
 594     copy.setText("Copy");
 595     copy.setMnemonic(KeyEvent.VK_C);
 596
 597     copy.addActionListener(new java.awt.event.ActionListener()
 598     {
 599       public void actionPerformed(ActionEvent e)
 600       {
 601         copy_actionPerformed(e);
 602       }
 603     });
 604     cut.setText("Cut");
 605     cut.setMnemonic(KeyEvent.VK_X);
 606     cut.addActionListener(new java.awt.event.ActionListener()
 607     {
 608       public void actionPerformed(ActionEvent e)
 609       {
 610         cut_actionPerformed(e);
 611       }
 612     });
 613     delete.setText("Delete");
 614     delete.addActionListener(new java.awt.event.ActionListener()
 615     {
 616       public void actionPerformed(ActionEvent e)
 617       {
 618         delete_actionPerformed(e);
 619       }
 620     });
 621     jMenu1.setMnemonic('V');
 622     jMenu1.setText("Paste");
 623     pasteNew.setText("to new alignment");
 624     pasteNew.addActionListener(new java.awt.event.ActionListener()
 625     {
 626       public void actionPerformed(ActionEvent e)
 627       {
 628         pasteNew_actionPerformed(e);
 629       }
 630     });
 631     pasteThis.setText("add to this alignment");
 632     pasteThis.addActionListener(new java.awt.event.ActionListener()
 633     {
 634       public void actionPerformed(ActionEvent e)
 635       {
 636         pasteThis_actionPerformed(e);
 637       }
 638     });
 639     applyToAllGroups.setText("Apply colour to all groups");
 640     applyToAllGroups.setState(true);
 641     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
 642     {
 643       public void actionPerformed(ActionEvent e)
 644       {
 645         applyToAllGroups_actionPerformed(e);
 646       }
 647     });
 648     createPNG.addActionListener(new java.awt.event.ActionListener()
 649     {
 650       public void actionPerformed(ActionEvent e)
 651       {
 652         createPNG_actionPerformed(e);
 653       }
 654     });
 655     createPNG.setActionCommand("Save as PNG Image");
 656     createPNG.setText("Save as PNG Image");
 657     font.setText("Change Font");
 658     font.addActionListener(new java.awt.event.ActionListener()
 659     {
 660       public void actionPerformed(ActionEvent e)
 661       {
 662         font_actionPerformed(e);
 663       }
 664     });
 665     fullSeqId.setText("Show full sequence id");
 666     fullSeqId.addActionListener(new java.awt.event.ActionListener()
 667     {
 668       public void actionPerformed(ActionEvent e)
 669       {
 670         fullSeqId_actionPerformed(e);
 671       }
 672     });
 673     epsFile.setText("Save as EPS file");
 674     epsFile.addActionListener(new java.awt.event.ActionListener()
 675     {
 676       public void actionPerformed(ActionEvent e)
 677       {
 678         epsFile_actionPerformed(e);
 679       }
 680     });
 681     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
 682     LoadtreeMenuItem.setText("Load assocated tree");
 683     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
 684       public void actionPerformed(ActionEvent e)
 685       {
 686         LoadtreeMenuItem_actionPerformed(e);
 687       }
 688     });
 689     jpred.setText("JPred");
 690     jpred.addActionListener(new java.awt.event.ActionListener()
 691     {
 692       public void actionPerformed(ActionEvent e)
 693       {
 694         jpred_actionPerformed(e);
 695       }
 696     });
 697     scaleAbove.setVisible(false);
 698     scaleAbove.setText("Scale above alignment");
 699     scaleAbove.addActionListener(new java.awt.event.ActionListener()
 700     {
 701       public void actionPerformed(ActionEvent e)
 702       {
 703         scaleAbove_actionPerformed(e);
 704       }
 705     });
 706     scaleLeft.setVisible(false);
 707     scaleLeft.setSelected(true);
 708     scaleLeft.setText("Scale left of sequence");
 709     scaleLeft.addActionListener(new java.awt.event.ActionListener()
 710     {
 711       public void actionPerformed(ActionEvent e)
 712       {
 713         scaleLeft_actionPerformed(e);
 714       }
 715     });
 716     scaleRight.setVisible(false);
 717     scaleRight.setSelected(true);
 718     scaleRight.setText("Scale right of sequence");
 719     scaleRight.addActionListener(new java.awt.event.ActionListener()
 720     {
 721       public void actionPerformed(ActionEvent e)
 722       {
 723         scaleRight_actionPerformed(e);
 724       }
 725     });
 726     modifyPID.setText("Modify PID Threshold");
 727     modifyPID.addActionListener(new java.awt.event.ActionListener()
 728     {
 729       public void actionPerformed(ActionEvent e)
 730       {
 731         modifyPID_actionPerformed(e);
 732       }
 733     });
 734     modifyConservation.setText("Modify Conservation Threshold");
 735     modifyConservation.addActionListener(new java.awt.event.ActionListener()
 736     {
 737       public void actionPerformed(ActionEvent e)
 738       {
 739         modifyConservation_actionPerformed(e);
 740       }
 741     });
 742     sortByTreeMenu.setText("Sort by tree order");
 743     alignFrameMenuBar.add(fileMenu);
 744     alignFrameMenuBar.add(editMenu);
 745     alignFrameMenuBar.add(searchMenu);
 746     alignFrameMenuBar.add(viewMenu);
 747     alignFrameMenuBar.add(colourMenu);
 748     alignFrameMenuBar.add(calculateMenu);
 749     alignFrameMenuBar.add(alignMenu);
 750     fileMenu.add(saveAlignmentMenu);
 751     fileMenu.add(outputTextboxMenu);
 752     fileMenu.add(htmlMenuItem);
 753     fileMenu.add(epsFile);
 754     fileMenu.add(createPNG);
 755     fileMenu.add(printMenuItem);
 756     fileMenu.addSeparator();
 757     fileMenu.add(LoadtreeMenuItem);
 758     fileMenu.addSeparator();
 759     fileMenu.add(closeMenuItem);
 760     editMenu.add(copy);
 761     editMenu.add(jMenu1);
 762     editMenu.add(cut);
 763     editMenu.add(delete);
 764     editMenu.addSeparator();
 765     editMenu.add(undoMenuItem);
 766     editMenu.add(redoMenuItem);
 767     editMenu.addSeparator();
 768     editMenu.add(deselectAllSequenceMenuItem);
 769     editMenu.add(selectAllSequenceMenuItem);
 770     editMenu.add(invertSequenceMenuItem);
 771     editMenu.add(deleteGroups);
 772     editMenu.addSeparator();
 773     editMenu.add(deselectAllColumnsMenuItem);
 774     editMenu.add(remove2LeftMenuItem);
 775     editMenu.add(remove2RightMenuItem);
 776     editMenu.addSeparator();
 777     editMenu.add(removeGappedColumnMenuItem);
 778     editMenu.add(removeAllGapsMenuItem);
 779     editMenu.add(setGapCharMenuItem);
 780     searchMenu.add(findMenuItem);
 781     viewMenu.add(font);
 782     viewMenu.add(fullSeqId);
 783     viewMenu.addSeparator();
 784     viewMenu.add(wrapMenuItem);
 785     viewMenu.add(scaleAbove);
 786     viewMenu.add(scaleLeft);
 787     viewMenu.add(scaleRight);
 788     viewMenu.addSeparator();
 789     viewMenu.add(viewBoxesMenuItem);
 790     viewMenu.add(viewTextMenuItem);
 791     viewMenu.add(colourTextMenuItem);
 792     viewMenu.add(renderGapsMenuItem);
 793     viewMenu.add(annotationPanelMenuItem);
 794     viewMenu.add(overviewMenuItem);
 795     viewMenu.add(sequenceFeatures);
 796     colourMenu.add(applyToAllGroups);
 797     colourMenu.add(noColourmenuItem);
 798     colourMenu.add(clustalColour);
 799     colourMenu.add(zappoColour);
 800     colourMenu.add(taylorColour);
 801     colourMenu.add(hydrophobicityColour);
 802     colourMenu.add(helixColour);
 803     colourMenu.add(strandColour);
 804     colourMenu.add(turnColour);
 805     colourMenu.add(buriedColour);
 806     colourMenu.add(nucleotideColour);
 807     colourMenu.add(userDefinedColour);
 808     colourMenu.add(PIDColour);
 809     colourMenu.add(BLOSUM62Colour);
 810     colourMenu.addSeparator();
 811     colourMenu.add(conservationMenuItem);
 812     colourMenu.add(modifyConservation);
 813     colourMenu.add(abovePIDThreshold);
 814     colourMenu.add(modifyPID);
 815     calculateMenu.add(sortPairwiseMenuItem);
 816     calculateMenu.add(sortIDMenuItem);
 817     calculateMenu.add(sortGroupMenuItem);
 818     calculateMenu.add(sortByTreeMenu);
 819     calculateMenu.add(removeRedundancyMenuItem);
 820     calculateMenu.addSeparator();
 821     calculateMenu.add(pairwiseAlignmentMenuItem);
 822     calculateMenu.add(PCAMenuItem);
 823     calculateMenu.addSeparator();
 824     calculateMenu.add(averageDistanceTreeMenuItem);
 825     calculateMenu.add(neighbourTreeMenuItem);
 826     calculateMenu.add(avDistanceTreeBlosumMenuItem);
 827     calculateMenu.add(njTreeBlosumMenuItem);
 828     alignMenu.add(clustalAlignMenuItem);
 829     alignMenu.add(msaAlignMenuItem);
 830     alignMenu.add(jpred);
 831     this.getContentPane().add(statusBar, BorderLayout.SOUTH);
 832     jMenu1.add(pasteNew);
 833     jMenu1.add(pasteThis);
 834   }
 835
 836   protected void saveAs_actionPerformed(ActionEvent e)
 837   {
 838
 839   }
 840
 841   protected void outputText_actionPerformed(ActionEvent e)
 842   {
 843
 844   }
 845
 846   protected void htmlMenuItem_actionPerformed(ActionEvent e)
 847   {
 848
 849   }
 850
 851
 852
 853
 854
 855   protected void closeMenuItem_actionPerformed(ActionEvent e)
 856   {
 857
 858   }
 859
 860   protected void redoMenuItem_actionPerformed(ActionEvent e)
 861   {
 862
 863   }
 864
 865   protected void undoMenuItem_actionPerformed(ActionEvent e)
 866   {
 867
 868   }
 869
 870
 871
 872
 873   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
 874   {
 875
 876   }
 877
 878   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
 879   {
 880
 881   }
 882
 883   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
 884   {
 885
 886   }
 887
 888
 889   protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
 890   {
 891
 892   }
 893
 894   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
 895   {
 896
 897   }
 898
 899   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
 900   {
 901
 902   }
 903
 904   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
 905   {
 906
 907   }
 908
 909   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
 910   {
 911
 912   }
 913
 914   protected void setGapCharMenuItem_actionPerformed(ActionEvent e)
 915   {
 916
 917   }
 918
 919
 920
 921
 922
 923   protected void wrapMenuItem_actionPerformed(ActionEvent e)
 924   {
 925
 926   }
 927
 928
 929   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
 930   {
 931
 932   }
 933
 934   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
 935   {
 936
 937   }
 938
 939
 940   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
 941   {
 942
 943   }
 944
 945
 946
 947   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
 948   {
 949
 950   }
 951
 952   protected void overviewMenuItem_actionPerformed(ActionEvent e)
 953   {
 954
 955   }
 956
 957   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
 958   {
 959
 960   }
 961
 962   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
 963   {
 964
 965   }
 966
 967   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
 968   {
 969
 970   }
 971
 972
 973   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
 974   {
 975
 976   }
 977
 978   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
 979   {
 980
 981   }
 982
 983   protected void PCAMenuItem_actionPerformed(ActionEvent e)
 984   {
 985
 986   }
 987
 988   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
 989   {
 990
 991   }
 992
 993   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
 994   {
 995
 996   }
 997
 998
 999   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1000   {
1001
1002   }
1003
1004   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
1005   {
1006
1007   }
1008
1009
1010
1011   protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
1012   {
1013
1014   }
1015
1016   protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
1017   {
1018
1019   }
1020
1021
1022   protected void clustalColour_actionPerformed(ActionEvent e)
1023   {
1024
1025   }
1026
1027   protected void zappoColour_actionPerformed(ActionEvent e)
1028   {
1029
1030   }
1031
1032   protected void taylorColour_actionPerformed(ActionEvent e)
1033   {
1034
1035   }
1036
1037
1038   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
1039   {
1040
1041   }
1042
1043   protected void helixColour_actionPerformed(ActionEvent e)
1044   {
1045
1046   }
1047
1048   protected void strandColour_actionPerformed(ActionEvent e)
1049   {
1050
1051   }
1052
1053   protected void turnColour_actionPerformed(ActionEvent e)
1054   {
1055
1056   }
1057
1058   protected void buriedColour_actionPerformed(ActionEvent e)
1059   {
1060
1061   }
1062
1063
1064
1065   protected void userDefinedColour_actionPerformed(ActionEvent e)
1066   {
1067
1068   }
1069
1070   protected void PIDColour_actionPerformed(ActionEvent e)
1071   {
1072
1073   }
1074
1075   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
1076   {
1077
1078   }
1079
1080
1081   protected void noColourmenuItem_actionPerformed(ActionEvent e)
1082   {
1083
1084   }
1085
1086   protected  void conservationMenuItem_actionPerformed(ActionEvent e)
1087   {
1088
1089   }
1090
1091
1092   protected void printMenuItem_actionPerformed(ActionEvent e)
1093   {
1094
1095   }
1096
1097   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
1098   {
1099
1100   }
1101
1102   protected void findMenuItem_actionPerformed(ActionEvent e)
1103   {
1104
1105   }
1106
1107
1108   protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
1109
1110   }
1111
1112   public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
1113   {
1114
1115   }
1116
1117   protected void nucleotideColour_actionPerformed(ActionEvent e)
1118   {
1119
1120   }
1121
1122   protected void deleteGroups_actionPerformed(ActionEvent e)
1123   {
1124
1125   }
1126
1127  protected void copy_actionPerformed(ActionEvent e)
1128   {
1129
1130   }
1131
1132
1133   protected void cut_actionPerformed(ActionEvent e)
1134   {
1135
1136   }
1137
1138   protected void delete_actionPerformed(ActionEvent e)
1139   {
1140
1141   }
1142
1143   protected void pasteNew_actionPerformed(ActionEvent e)
1144   {
1145
1146   }
1147
1148   protected void pasteThis_actionPerformed(ActionEvent e)
1149   {
1150
1151   }
1152
1153   protected void applyToAllGroups_actionPerformed(ActionEvent e)
1154   {
1155
1156   }
1157
1158   protected void createPNG_actionPerformed(ActionEvent e)
1159   {
1160
1161   }
1162
1163   protected void font_actionPerformed(ActionEvent e)
1164   {
1165
1166   }
1167
1168   protected void fullSeqId_actionPerformed(ActionEvent e)
1169   {
1170
1171   }
1172
1173   protected void epsFile_actionPerformed(ActionEvent e)
1174   {
1175
1176   }
1177
1178   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
1179
1180   }
1181
1182   protected void jpred_actionPerformed(ActionEvent e)
1183   {
1184
1185   }
1186
1187   protected void scaleAbove_actionPerformed(ActionEvent e)
1188   {
1189
1190   }
1191
1192   protected void scaleLeft_actionPerformed(ActionEvent e)
1193   {
1194
1195   }
1196
1197   protected void scaleRight_actionPerformed(ActionEvent e)
1198   {
1199
1200   }
1201
1202   protected void modifyPID_actionPerformed(ActionEvent e)
1203   {
1204
1205   }
1206
1207   protected void modifyConservation_actionPerformed(ActionEvent e)
1208   {
1209
1210   }
1211
1212
1213
1214
1215 }